danilovkiri
- Total activity 116
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 13
- Subscriptions 30
Comments
Recent activity by danilovkiri Sort by recent activity-
Hi Ganesh P Kumar I guess there is nothing to be done here given your reference genome size. BwaMemIndexImageCreator does basically the same as `bwa index -a bwtsw` which takes a couple of hours fo...
-
Hi William Brown First, it is incorrect to call such data transformation as conversion. The data in VCF and fasta are nonequivalent. Second, googling can help. There is the same question on biosta...
-
An index can be created on coordinate-sorted files only. MarkDuplicates does not require a BAI index for an input BAM file.
-
Have you read the doc https://gatk.broadinstitute.org/hc/en-us/articles/360037426651-ReorderSam-Picard-? Googling a tool prior to its usage is a great way to understand what it actually does. The m...
-
Hi. Try to tun 'bcftools norm` prior to liftovering. It might be of help. Also, have a look at the rejected VCF file (there is an argument REJECT to specify the file which will contain all rejecte...
-
vctrymao The exception explicitly states that the BAM files should be sorted by queryname. Can you confirm that the input BAM files are queryname sorted? If not, `samtools sort -n` will help.
-
Vincent Appiah You have to gzip the VCF file (if not already done, if it is unzipped, then why?) and use tabix <file.vcf.gz> or bcftools index --tbi <filename> The tbi index is perfectly fine. You ...
-
Hi Linda Do Such simple tasks do not require such complex solutions. There is a BCFtools package for any manipulations with VCF files. All you have to do is to run bcftools view -O v -o <output_vcf...
-
Bhanu Gandham Thank you!
-
Hi Sara Coder The answer to your first question can be easily googled since the filenames contain the corresponding study names in which the VCFs were obtained/generated. As for the second question...